[CIG-SHORT] I/O error while reading SimpleDB data.
Brad Aagaard
baagaard at usgs.gov
Thu Apr 11 15:18:49 PDT 2013
You need to make sure your data points span the spatial extent of the
BC. Each point for the BC will be projected onto the virtual line
associated with the spatial database.
Regards,
Brad
On 04/11/2013 02:52 PM, Adewale Moroof Amosu (amamosu) wrote:
> It worked when I change the num-locs however if I use the "linear" interpolation rather than "nearest" in the file step18.cfg it gives the following error:
>
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/utils/PetscManager.py:64:initialize
> -- petsc(info)
> -- Initialized PETSc.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/meshio/MeshIOObj.py:55:read
> -- meshiocubit(info)
> -- Reading finite-element mesh
> >> meshio/MeshIOCubit.cc:142:<unknown>
> -- meshiocubit(info)
> -- Reading 245 vertices.
> >> meshio/MeshIOCubit.cc:197:<unknown>
> -- meshiocubit(info)
> -- Reading 144 cells in 2 blocks.
> >> meshio/MeshIOCubit.cc:257:<unknown>
> -- meshiocubit(info)
> -- Found 8 node sets.
> >> meshio/MeshIOCubit.cc:285:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'fault' with id 10 containing 35 nodes.
> >> meshio/MeshIOCubit.cc:285:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'face_xpos' with id 11 containing 35 nodes.
> >> meshio/MeshIOCubit.cc:285:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'face_xneg' with id 12 containing 35 nodes.
> >> meshio/MeshIOCubit.cc:285:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'face_ypos' with id 13 containing 35 nodes.
> >> meshio/MeshIOCubit.cc:285:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'face_yneg' with id 14 containing 35 nodes.
> >> meshio/MeshIOCubit.cc:285:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'face_zneg' with id 15 containing 49 nodes.
> >> meshio/MeshIOCubit.cc:285:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'face_zneg_nofault' with id 16 containing 42 nodes.
> >> meshio/MeshIOCubit.cc:285:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'face_zpos' with id 17 containing 49 nodes.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:92:preinitialize
> -- timedependent(info)
> -- Pre-initializing problem.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:389:_setupMaterials
> -- implicit(info)
> -- Pre-initializing materials.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/feassemble/FIATLagrange.py:407:initialize
> -- fiatlagrange(info)
> -- Cell geometry:
> -- <pylith.feassemble.CellGeometry.GeometryHex3D; proxy of <Swig Object of type 'pylith::feassemble::GeometryHex3D *' at 0x10626a9c0> >
> -- Vertices:
> -- [[-1. -1. -1.]
> [ 1. -1. -1.]
> [ 1. 1. -1.]
> [-1. 1. -1.]
> [-1. -1. 1.]
> [ 1. -1. 1.]
> [ 1. 1. 1.]
> [-1. 1. 1.]]
> -- Quad pts:
> -- [[-0.57735027 -0.57735027 -0.57735027]
> [ 0.57735027 -0.57735027 -0.57735027]
> [-0.57735027 0.57735027 -0.57735027]
> [ 0.57735027 0.57735027 -0.57735027]
> [-0.57735027 -0.57735027 0.57735027]
> [ 0.57735027 -0.57735027 0.57735027]
> [-0.57735027 0.57735027 0.57735027]
> [ 0.57735027 0.57735027 0.57735027]]
> -- Quad wts:
> -- [ 1. 1. 1. 1. 1. 1. 1. 1.]
> -- Basis fns @ quad pts ):
> -- [[ 0.49056261 0.13144586 0.03522081 0.13144586 0.13144586 0.03522081
> 0.00943739 0.03522081]
> [ 0.13144586 0.49056261 0.13144586 0.03522081 0.03522081 0.13144586
> 0.03522081 0.00943739]
> [ 0.13144586 0.03522081 0.13144586 0.49056261 0.03522081 0.00943739
> 0.03522081 0.13144586]
> [ 0.03522081 0.13144586 0.49056261 0.13144586 0.00943739 0.03522081
> 0.13144586 0.03522081]
> [ 0.13144586 0.03522081 0.00943739 0.03522081 0.49056261 0.13144586
> 0.03522081 0.13144586]
> [ 0.03522081 0.13144586 0.03522081 0.00943739 0.13144586 0.49056261
> 0.13144586 0.03522081]
> [ 0.03522081 0.00943739 0.03522081 0.13144586 0.13144586 0.03522081
> 0.13144586 0.49056261]
> [ 0.00943739 0.03522081 0.13144586 0.03522081 0.03522081 0.13144586
> 0.49056261 0.13144586]]
> -- Basis fn derivatives @ quad pts:
> -- [[[-0.31100423 -0.31100423 -0.31100423]
> [ 0.31100423 -0.08333333 -0.08333333]
> [ 0.08333333 0.08333333 -0.0223291 ]
> [-0.08333333 0.31100423 -0.08333333]
> [-0.08333333 -0.08333333 0.31100423]
> [ 0.08333333 -0.0223291 0.08333333]
> [ 0.0223291 0.0223291 0.0223291 ]
> [-0.0223291 0.08333333 0.08333333]]
>
> [[-0.31100423 -0.08333333 -0.08333333]
> [ 0.31100423 -0.31100423 -0.31100423]
> [ 0.08333333 0.31100423 -0.08333333]
> [-0.08333333 0.08333333 -0.0223291 ]
> [-0.08333333 -0.0223291 0.08333333]
> [ 0.08333333 -0.08333333 0.31100423]
> [ 0.0223291 0.08333333 0.08333333]
> [-0.0223291 0.0223291 0.0223291 ]]
>
> [[-0.08333333 -0.31100423 -0.08333333]
> [ 0.08333333 -0.08333333 -0.0223291 ]
> [ 0.31100423 0.08333333 -0.08333333]
> [-0.31100423 0.31100423 -0.31100423]
> [-0.0223291 -0.08333333 0.08333333]
> [ 0.0223291 -0.0223291 0.0223291 ]
> [ 0.08333333 0.0223291 0.08333333]
> [-0.08333333 0.08333333 0.31100423]]
>
> [[-0.08333333 -0.08333333 -0.0223291 ]
> [ 0.08333333 -0.31100423 -0.08333333]
> [ 0.31100423 0.31100423 -0.31100423]
> [-0.31100423 0.08333333 -0.08333333]
> [-0.0223291 -0.0223291 0.0223291 ]
> [ 0.0223291 -0.08333333 0.08333333]
> [ 0.08333333 0.08333333 0.31100423]
> [-0.08333333 0.0223291 0.08333333]]
>
> [[-0.08333333 -0.08333333 -0.31100423]
> [ 0.08333333 -0.0223291 -0.08333333]
> [ 0.0223291 0.0223291 -0.0223291 ]
> [-0.0223291 0.08333333 -0.08333333]
> [-0.31100423 -0.31100423 0.31100423]
> [ 0.31100423 -0.08333333 0.08333333]
> [ 0.08333333 0.08333333 0.0223291 ]
> [-0.08333333 0.31100423 0.08333333]]
>
> [[-0.08333333 -0.0223291 -0.08333333]
> [ 0.08333333 -0.08333333 -0.31100423]
> [ 0.0223291 0.08333333 -0.08333333]
> [-0.0223291 0.0223291 -0.0223291 ]
> [-0.31100423 -0.08333333 0.08333333]
> [ 0.31100423 -0.31100423 0.31100423]
> [ 0.08333333 0.31100423 0.08333333]
> [-0.08333333 0.08333333 0.0223291 ]]
>
> [[-0.0223291 -0.08333333 -0.08333333]
> [ 0.0223291 -0.0223291 -0.0223291 ]
> [ 0.08333333 0.0223291 -0.08333333]
> [-0.08333333 0.08333333 -0.31100423]
> [-0.08333333 -0.31100423 0.08333333]
> [ 0.08333333 -0.08333333 0.0223291 ]
> [ 0.31100423 0.08333333 0.08333333]
> [-0.31100423 0.31100423 0.31100423]]
>
> [[-0.0223291 -0.0223291 -0.0223291 ]
> [ 0.0223291 -0.08333333 -0.08333333]
> [ 0.08333333 0.08333333 -0.31100423]
> [-0.08333333 0.0223291 -0.08333333]
> [-0.08333333 -0.08333333 0.0223291 ]
> [ 0.08333333 -0.31100423 0.08333333]
> [ 0.31100423 0.31100423 0.31100423]
> [-0.31100423 0.08333333 0.08333333]]]
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:403:_setupMaterials
> -- implicit(info)
> -- Added elasticity integrator for material 'Lower crust material'.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/feassemble/FIATLagrange.py:407:initialize
> -- fiatlagrange(info)
> -- Cell geometry:
> -- <pylith.feassemble.CellGeometry.GeometryHex3D; proxy of <Swig Object of type 'pylith::feassemble::GeometryHex3D *' at 0x1062e9ed0> >
> -- Vertices:
> -- [[-1. -1. -1.]
> [ 1. -1. -1.]
> [ 1. 1. -1.]
> [-1. 1. -1.]
> [-1. -1. 1.]
> [ 1. -1. 1.]
> [ 1. 1. 1.]
> [-1. 1. 1.]]
> -- Quad pts:
> -- [[-0.57735027 -0.57735027 -0.57735027]
> [ 0.57735027 -0.57735027 -0.57735027]
> [-0.57735027 0.57735027 -0.57735027]
> [ 0.57735027 0.57735027 -0.57735027]
> [-0.57735027 -0.57735027 0.57735027]
> [ 0.57735027 -0.57735027 0.57735027]
> [-0.57735027 0.57735027 0.57735027]
> [ 0.57735027 0.57735027 0.57735027]]
> -- Quad wts:
> -- [ 1. 1. 1. 1. 1. 1. 1. 1.]
> -- Basis fns @ quad pts ):
> -- [[ 0.49056261 0.13144586 0.03522081 0.13144586 0.13144586 0.03522081
> 0.00943739 0.03522081]
> [ 0.13144586 0.49056261 0.13144586 0.03522081 0.03522081 0.13144586
> 0.03522081 0.00943739]
> [ 0.13144586 0.03522081 0.13144586 0.49056261 0.03522081 0.00943739
> 0.03522081 0.13144586]
> [ 0.03522081 0.13144586 0.49056261 0.13144586 0.00943739 0.03522081
> 0.13144586 0.03522081]
> [ 0.13144586 0.03522081 0.00943739 0.03522081 0.49056261 0.13144586
> 0.03522081 0.13144586]
> [ 0.03522081 0.13144586 0.03522081 0.00943739 0.13144586 0.49056261
> 0.13144586 0.03522081]
> [ 0.03522081 0.00943739 0.03522081 0.13144586 0.13144586 0.03522081
> 0.13144586 0.49056261]
> [ 0.00943739 0.03522081 0.13144586 0.03522081 0.03522081 0.13144586
> 0.49056261 0.13144586]]
> -- Basis fn derivatives @ quad pts:
> -- [[[-0.31100423 -0.31100423 -0.31100423]
> [ 0.31100423 -0.08333333 -0.08333333]
> [ 0.08333333 0.08333333 -0.0223291 ]
> [-0.08333333 0.31100423 -0.08333333]
> [-0.08333333 -0.08333333 0.31100423]
> [ 0.08333333 -0.0223291 0.08333333]
> [ 0.0223291 0.0223291 0.0223291 ]
> [-0.0223291 0.08333333 0.08333333]]
>
> [[-0.31100423 -0.08333333 -0.08333333]
> [ 0.31100423 -0.31100423 -0.31100423]
> [ 0.08333333 0.31100423 -0.08333333]
> [-0.08333333 0.08333333 -0.0223291 ]
> [-0.08333333 -0.0223291 0.08333333]
> [ 0.08333333 -0.08333333 0.31100423]
> [ 0.0223291 0.08333333 0.08333333]
> [-0.0223291 0.0223291 0.0223291 ]]
>
> [[-0.08333333 -0.31100423 -0.08333333]
> [ 0.08333333 -0.08333333 -0.0223291 ]
> [ 0.31100423 0.08333333 -0.08333333]
> [-0.31100423 0.31100423 -0.31100423]
> [-0.0223291 -0.08333333 0.08333333]
> [ 0.0223291 -0.0223291 0.0223291 ]
> [ 0.08333333 0.0223291 0.08333333]
> [-0.08333333 0.08333333 0.31100423]]
>
> [[-0.08333333 -0.08333333 -0.0223291 ]
> [ 0.08333333 -0.31100423 -0.08333333]
> [ 0.31100423 0.31100423 -0.31100423]
> [-0.31100423 0.08333333 -0.08333333]
> [-0.0223291 -0.0223291 0.0223291 ]
> [ 0.0223291 -0.08333333 0.08333333]
> [ 0.08333333 0.08333333 0.31100423]
> [-0.08333333 0.0223291 0.08333333]]
>
> [[-0.08333333 -0.08333333 -0.31100423]
> [ 0.08333333 -0.0223291 -0.08333333]
> [ 0.0223291 0.0223291 -0.0223291 ]
> [-0.0223291 0.08333333 -0.08333333]
> [-0.31100423 -0.31100423 0.31100423]
> [ 0.31100423 -0.08333333 0.08333333]
> [ 0.08333333 0.08333333 0.0223291 ]
> [-0.08333333 0.31100423 0.08333333]]
>
> [[-0.08333333 -0.0223291 -0.08333333]
> [ 0.08333333 -0.08333333 -0.31100423]
> [ 0.0223291 0.08333333 -0.08333333]
> [-0.0223291 0.0223291 -0.0223291 ]
> [-0.31100423 -0.08333333 0.08333333]
> [ 0.31100423 -0.31100423 0.31100423]
> [ 0.08333333 0.31100423 0.08333333]
> [-0.08333333 0.08333333 0.0223291 ]]
>
> [[-0.0223291 -0.08333333 -0.08333333]
> [ 0.0223291 -0.0223291 -0.0223291 ]
> [ 0.08333333 0.0223291 -0.08333333]
> [-0.08333333 0.08333333 -0.31100423]
> [-0.08333333 -0.31100423 0.08333333]
> [ 0.08333333 -0.08333333 0.0223291 ]
> [ 0.31100423 0.08333333 0.08333333]
> [-0.31100423 0.31100423 0.31100423]]
>
> [[-0.0223291 -0.0223291 -0.0223291 ]
> [ 0.0223291 -0.08333333 -0.08333333]
> [ 0.08333333 0.08333333 -0.31100423]
> [-0.08333333 0.0223291 -0.08333333]
> [-0.08333333 -0.08333333 0.0223291 ]
> [ 0.08333333 -0.31100423 0.08333333]
> [ 0.31100423 0.31100423 0.31100423]
> [-0.31100423 0.08333333 0.08333333]]]
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:403:_setupMaterials
> -- implicit(info)
> -- Added elasticity integrator for material 'Upper crust material'.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:419:_setupBC
> -- implicit(info)
> -- Pre-initializing boundary conditions.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/feassemble/FIATLagrange.py:407:initialize
> -- fiatlagrange(info)
> -- Cell geometry:
> -- <pylith.feassemble.CellGeometry.GeometryQuad3D; proxy of <Swig Object of type 'pylith::feassemble::GeometryQuad3D *' at 0x1062ef330> >
> -- Vertices:
> -- [[-1. -1.]
> [ 1. -1.]
> [ 1. 1.]
> [-1. 1.]]
> -- Quad pts:
> -- [[-0.57735027 -0.57735027]
> [ 0.57735027 -0.57735027]
> [-0.57735027 0.57735027]
> [ 0.57735027 0.57735027]]
> -- Quad wts:
> -- [ 1. 1. 1. 1.]
> -- Basis fns @ quad pts ):
> -- [[ 0.62200847 0.16666667 0.0446582 0.16666667]
> [ 0.16666667 0.62200847 0.16666667 0.0446582 ]
> [ 0.16666667 0.0446582 0.16666667 0.62200847]
> [ 0.0446582 0.16666667 0.62200847 0.16666667]]
> -- Basis fn derivatives @ quad pts:
> -- [[[-0.39433757 -0.39433757]
> [ 0.39433757 -0.10566243]
> [ 0.10566243 0.10566243]
> [-0.10566243 0.39433757]]
>
> [[-0.39433757 -0.10566243]
> [ 0.39433757 -0.39433757]
> [ 0.10566243 0.39433757]
> [-0.10566243 0.10566243]]
>
> [[-0.10566243 -0.39433757]
> [ 0.10566243 -0.10566243]
> [ 0.39433757 0.10566243]
> [-0.39433757 0.39433757]]
>
> [[-0.10566243 -0.10566243]
> [ 0.10566243 -0.39433757]
> [ 0.39433757 0.39433757]
> [-0.39433757 0.10566243]]]
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:432:_setupBC
> -- implicit(info)
> -- Added boundary condition 'face_zpos' as an integrator.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:438:_setupBC
> -- implicit(info)
> -- Added boundary condition 'face_xpos' as a constraint.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:438:_setupBC
> -- implicit(info)
> -- Added boundary condition 'face_xneg' as a constraint.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:438:_setupBC
> -- implicit(info)
> -- Added boundary condition 'face_zneg' as a constraint.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:438:_setupBC
> -- implicit(info)
> -- Added boundary condition 'face_ypos' as a constraint.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:438:_setupBC
> -- implicit(info)
> -- Added boundary condition 'face_yneg' as a constraint.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:458:_setupInterfaces
> -- implicit(info)
> -- Pre-initializing interior interfaces.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:187:preinitialize
> -- implicit(info)
> -- Pre-initializing output.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Problem.py:150:verifyConfiguration
> -- timedependent(info)
> -- Verifying compatibility of problem configuration.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:117:initialize
> -- timedependent(info)
> -- Initializing problem.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:499:_initialize
> -- implicit(info)
> -- Initializing integrators.
> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/bc/Neumann.py:134:initialize
> -- timedependent(info)
> -- Initializing Neumann boundary 'face_zpos'.
> Fatal error. Calling MPI_Abort() to abort PyLith application.
> Traceback (most recent call last):
> File "/Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 65, in onComputeNodes
> self.main(*args, **kwds)
> File "/Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/apps/PyLithApp.py", line 113, in main
> self.problem.initialize()
> File "/Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/TimeDependent.py", line 119, in initialize
> self.formulation.initialize(self.dimension, self.normalizer)
> File "/Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Implicit.py", line 127, in initialize
> self._initialize(dimension, normalizer)
> File "/Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py", line 503, in _initialize
> integrator.initialize(totalTime, numTimeSteps, normalizer)
> File "/Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/bc/Neumann.py", line 137, in initialize
> BoundaryCondition.initialize(self, totalTime, numTimeSteps, normalizer)
> File "/Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/bc/BoundaryCondition.py", line 127, in initialize
> ModuleBoundaryCondition.initialize(self, self.mesh, self.upDir)
> File "/Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/bc/bc.py", line 154, in initialize
> def initialize(self, *args): return _bc.BoundaryCondition_initialize(self, *args)
> RuntimeError: Could not find values at ( 211.325 2211.32 0) for traction boundary condition face_zpos
> using spatial database Neumann BC on +z.
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/bin/nemesis: mpirun: exit 255
> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/bin/pylith: /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/bin/nemesis: exit 1
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> Thanks , I changed the num-locs to the current number but im not sure what a line feed is or how to end the file
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>
> A. Amosu
> Center for Earthquake Research and Information (CERI)
> University of Memphis
> Memphis, TN
> USA
> ________________________________________
> From: Brad Aagaard [baagaard at usgs.gov]
> Sent: Thursday, April 11, 2013 4:30 PM
> To: Adewale Moroof Amosu (amamosu); cig-short at geodynamics.org
> Subject: Re: I/O error while reading SimpleDB data.
>
> Yes, you can create a linear variation in the axial load. You need to
> add a line feed at the end of the file. See
> http://www.geodynamics.org/cig/community/workinggroups/short/workarea/pylith-wiki/index_html#errors_spatialdata
>
> I have made the error message more verbose to suggest the proper fixes.
> This will appear in the next release.
>
> Brad
>
>
> On 04/11/2013 09:35 AM, Adewale Moroof Amosu (amamosu) wrote:
>> I am trying to modify the step18 example in the pylith manual.
>>
>> The example does surface loading for a point.
>> I am trying to extend it to surface loading for a line.
>>
>> When I use the points from the line only it gives me an I/O error. However when I add other points outside the line it works.
>>
>> Is there a way to do it for just the line?
>>
>> I have attached two folders one that works and the one that doesn't work. The only difference are the points that I put in the spatialdb/tractions_axial_pressure.spatialdb file.
>>
>> I have also attached the result for the one that works and another plot of the line. The red dots show the line and the blue points show the extra points added for it to work.
>>
>> Here is a copy of the error message:
> -- OUTPUT DELETED --
>> >> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/bc/Neumann.py:134:initialize
>> -- timedependent(info)
>> -- Initializing Neumann boundary 'face_zpos'.
>> Fatal error. Calling MPI_Abort() to abort PyLith application.
>> Traceback (most recent call last):
>> File "/Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 65, in onComputeNodes
>> self.main(*args, **kwds)
>> File "/Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/apps/PyLithApp.py", line 113, in main
>> self.problem.initialize()
>> File "/Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/TimeDependent.py", line 119, in initialize
>> self.formulation.initialize(self.dimension, self.normalizer)
>> File "/Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Implicit.py", line 127, in initialize
>> self._initialize(dimension, normalizer)
>> File "/Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py", line 503, in _initialize
>> integrator.initialize(totalTime, numTimeSteps, normalizer)
>> File "/Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/bc/Neumann.py", line 137, in initialize
>> BoundaryCondition.initialize(self, totalTime, numTimeSteps, normalizer)
>> File "/Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/bc/BoundaryCondition.py", line 127, in initialize
>> ModuleBoundaryCondition.initialize(self, self.mesh, self.upDir)
>> File "/Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/lib/python2.7/site-packages/pylith/bc/bc.py", line 154, in initialize
>> def initialize(self, *args): return _bc.BoundaryCondition_initialize(self, *args)
>> RuntimeError: Error occurred while reading spatial database file 'spatialdb/tractions_axial_pressure.spatialdb'.
>> I/O error while reading SimpleDB data.
>> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
>> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/bin/nemesis: mpirun: exit 255
>> /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/bin/pylith: /Users/adewaleamosu/src/pylith/pylith-1.7.1-darwin-10.6.8/bin/nemesis: exit 1
>>
>>
>>
>>
>> Thanks
>> Adewale
>>
>
>
>
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